Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps

Sung Wook Chi, Julie B. Zang, Aldo Mele, Robert B. Darnell

Research output: Contribution to journalArticlepeer-review

1283 Citations (Scopus)

Abstract

MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets - Ago-miRNA and Ago-mRNA binding sites - that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.

Original languageEnglish
Pages (from-to)479-486
Number of pages8
JournalNature
Volume460
Issue number7254
DOIs
Publication statusPublished - 2009 Jul 23
Externally publishedYes

ASJC Scopus subject areas

  • General

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